Well I've had a chance to play a good deal of SP and MP 1.09 and my general feeling is that, while there are certainly minor improvements, 1.09 isn't what I had hoped.  Since this is just the BETA of the 1.1 patch, I can only hope that some of the things mentioned below will be corrected/added.

Balance Issues
Single player is a lot more challenging.  I used to be able to take on any number of Hard AI without issue, but now they pretty much stomp me unless I have a perfect game.  Easy is a joke and normal is not tough enough, IMO.  Unfair is well, unfair

AI of all races overuse fighters and bombers, period.  That could be because fighters and bombers are so much more powerful in 1.09, and the AI is just smartly exploiting that.  I can't tell you how many times I had to rush drone hosts in SP.  Flak frigates are now absolutely useless vs fighters/bombers.  I built flaks at a 2-1 ratio vs an enemy fleet of mostly carriers and they got stomped (my flaks).  It's no fun if the AI uses the same attack method over and over, regardless of the situation.  Hanger defenses are pretty much useless as a static defense vs strike craft because the fighters and bombers almost never attack each other - they fly right past each other on their way to other targets - usually ones you wouldn't manually choose.  In general, I think strike craft should concentrate on each other first - then take out other vessels.  They have never done this.

Guass cannons seem a bit more potent now.  AI fleets will turn away from a heavily guassed planet, even when they shouldn't.  Apparently no one thought to give AI the ability to scope out the situation and simply attack from the side of the planet where there are no cannons.  In general, AI does a poor job of picking out Targets of Opportunity.

Networking / Multiplayer
I played around 10 MP matches with 1.09 and in every match but one my opponents left or were dropped.  That doesn't say much for the Alloy system.  It's hard enough to FIND someone playing online with 1.09, so having them drop is especially painful.  They didn't just get disconnected, most of them complained that their connection was really slow and then they dropped manually.  Either way, there is still work to be done on the netcode end.  I never had anyone complain about not being able to join or host a server though, but like I said, there was never any more than a dozen players online and most of them were in the few games being played.

Bugs / Opinions
There are still a number of annoying issues.  Things like being told your planet is under seige when an enemy scout is in the radius are still happening.  You are always told that "pirates are raiding our planet" or whatever, even if they are just passing through it.  These are obvious bugs that have always existed.

I think the new resource window is handy, but much too large.  Reduce it in size by at least 30% and add the name of the enemy bounty is being placed on (and who is placing it on me), so I know who I'm dealing with.  It would also be nice if I could choose the enemy from a drop-down here, so I don't have to open up the Pirate menu to choose.

I still think cap ships need to be stronger, especially in the planetary bombardment category.  Not much, just maybe 25% more damage vs planets across the board would make a huge difference.

Ally attack and defence pings don't seem to work, no matter what keys I map them to.  This makes it impossible for me to ask my AI allys to help me.

When are we going to have a way to send or ask for resources from allies?  I'm very dissapointed that this still hasn't been implemented.

Why isn't there an option to hand over your planets/fleet to an ally when you leave the game?  This just seems logical.  It would certainly make losing a teammate in a game much easier to swallow.

Cap ships still get distracted from planetary bombardment even if a lame scout comes into the radius.  This really needs to be addressed.

What Works / Final Thoughts
I like the new explosions.  I wish there were more, and I wish there were more types or variations of planets.  It detracts from the believability when each Terran planet looks the same   The econ system seems a bit more balanced, and I find myself working for more than just credits as I was before the patch.  I used to simply bulk up on trade ports and buy anything I needed, but it's easier to harvest normally now.  Cap ships now automatically attack planets if all enemy ships are destroyed, which is nice, and the rest of the fleet cleans up the buildings automatically rather than just sitting there. 

I feel that 1.09 is a step forward, just not a very large step.  I hope they make more significant changes/additions prior to the formal 1.1 release!